CST6 (cystatin E/M) - Rat Genome Database
Submit Data |  Help |  Video Tutorials |  News |  Publications |  FTP Download |  REST API |  Citing RGD |  Contact   
Gene: CST6 (cystatin E/M) Homo sapiens
Analyze
Symbol: CST6
Name: cystatin E/M
RGD ID: 1352727
HGNC Page HGNC
Description: Predicted to have cysteine-type endopeptidase inhibitor activity. Predicted to be involved in anatomical structure morphogenesis. Localizes to extracellular exosome. Implicated in ectodermal dysplasia 15.
Type: protein-coding
RefSeq Status: REVIEWED
Also known as: cystatin 6; cystatin M; cystatin M/E; cystatin-6; cystatin-E; cystatin-M; cysteine proteinase inhibitor; ECTD15
RGD Orthologs
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1166,012,008 - 66,013,505 (+)EnsemblGRCh38hg38GRCh38
GRCh381166,012,008 - 66,013,505 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371165,779,479 - 65,780,976 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361165,536,038 - 65,537,552 (+)NCBINCBI36hg18NCBI36
Build 341165,536,037 - 65,537,551NCBI
Celera1163,104,649 - 63,105,332 (+)NCBI
Cytogenetic Map11q13.1NCBI
HuRef1162,105,544 - 62,107,045 (+)NCBIHuRef
CHM1_11165,663,579 - 65,665,098 (+)NCBICHM1_1
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

Phenotype Annotations     Click to see Annotation Detail View

Human Phenotype
References

References - curated
1. GOA_HUMAN data from the GO Consortium
2. RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:2029847   PMID:3202964   PMID:8179826   PMID:8995380   PMID:9007972   PMID:9099741   PMID:9154125   PMID:11348457   PMID:12477932   PMID:12839564   PMID:14676833   PMID:14702039  
PMID:15466187   PMID:15489334   PMID:16356477   PMID:16565075   PMID:16912163   PMID:17043665   PMID:17099723   PMID:17540367   PMID:18506750   PMID:18607344   PMID:18676742   PMID:18754876  
PMID:19005484   PMID:19074894   PMID:19262604   PMID:19503093   PMID:19551853   PMID:20074384   PMID:21092257   PMID:21900206   PMID:22688893   PMID:22902879   PMID:23006792   PMID:23088560  
PMID:23376485   PMID:23533145   PMID:23537643   PMID:24742492   PMID:24927181   PMID:25640309   PMID:26186194   PMID:26485645   PMID:27090639   PMID:27173435   PMID:28514442   PMID:28630039  
PMID:29229926   PMID:29509190   PMID:29530995   PMID:30425301   PMID:32296183  


Genomics

Comparative Map Data
CST6
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1166,012,008 - 66,013,505 (+)EnsemblGRCh38hg38GRCh38
GRCh381166,012,008 - 66,013,505 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371165,779,479 - 65,780,976 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361165,536,038 - 65,537,552 (+)NCBINCBI36hg18NCBI36
Build 341165,536,037 - 65,537,551NCBI
Celera1163,104,649 - 63,105,332 (+)NCBI
Cytogenetic Map11q13.1NCBI
HuRef1162,105,544 - 62,107,045 (+)NCBIHuRef
CHM1_11165,663,579 - 65,665,098 (+)NCBICHM1_1
Cst6
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39195,394,733 - 5,399,602 (-)NCBIGRCm39mm39
GRCm39 Ensembl195,394,733 - 5,399,602 (-)Ensembl
GRCm38195,344,705 - 5,349,574 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl195,344,705 - 5,349,574 (-)EnsemblGRCm38mm10GRCm38
MGSCv37195,344,705 - 5,349,574 (-)NCBIGRCm37mm9NCBIm37
MGSCv36195,344,705 - 5,349,574 (-)NCBImm8
Celera195,216,597 - 5,221,470 (-)NCBICelera
Cytogenetic Map19ANCBI
cM Map194.3NCBI
Cst6
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21202,655,322 - 202,657,030 (-)NCBI
Rnor_6.0 Ensembl1220,727,292 - 220,729,000 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01220,727,292 - 220,729,000 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01227,656,559 - 227,658,267 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41207,991,313 - 207,993,021 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11208,144,765 - 208,146,474 (-)NCBI
Celera1200,190,620 - 200,192,328 (-)NCBICelera
Cytogenetic Map1q43NCBI
Cst6
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542219,313,352 - 19,327,360 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495542219,326,302 - 19,327,449 (-)NCBIChiLan1.0ChiLan1.0
CST6
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11164,703,367 - 64,704,865 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1164,703,412 - 64,704,762 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01161,375,744 - 61,377,909 (+)NCBIMhudiblu_PPA_v0panPan3
CST6
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl1851,263,178 - 51,264,780 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.11851,263,161 - 51,264,816 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Cst6
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049365993,541,359 - 3,543,206 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CST6
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl26,323,737 - 6,325,477 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.126,323,737 - 6,325,519 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.225,427,434 - 5,429,216 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CST6
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.118,244,483 - 8,246,551 (-)NCBI
ChlSab1.1 Ensembl18,244,485 - 8,245,968 (-)Ensembl
Cst6
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462476720,423,007 - 20,424,773 (-)NCBI

Position Markers
RH71245  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371165,780,320 - 65,780,862UniSTSGRCh37
Build 361165,536,896 - 65,537,438RGDNCBI36
Celera1163,104,676 - 63,105,218RGD
Cytogenetic Map11q13UniSTS
HuRef1162,106,389 - 62,106,931UniSTS
GeneMap99-GB4 RH Map11247.67UniSTS
NCBI RH Map11573.2UniSTS

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:303
Count of miRNA genes:286
Interacting mature miRNAs:303
Transcripts:ENST00000312134
Prediction methods:Miranda, Rnahybrid
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system sensory system adipose tissue appendage entire extraembryonic component
High 1 1 2 324 1 6 117
Medium 33 942 639 38 3 14 1375 12 6 46 272 1248 36 84 965 1
Low 1190 967 421 157 314 37 1575 941 1719 200 943 251 120 584 1124 3
Below cutoff 1040 892 426 242 925 229 946 1101 1667 133 190 66 15 481 540 1

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000312134   ⟹   ENSP00000311313
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl1166,012,008 - 66,013,505 (+)Ensembl
RefSeq Acc Id: NM_001323   ⟹   NP_001314
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381166,012,008 - 66,013,505 (+)NCBI
GRCh371165,779,462 - 65,780,976 (+)ENTREZGENE
Build 361165,536,038 - 65,537,552 (+)NCBI Archive
HuRef1162,105,544 - 62,107,045 (+)ENTREZGENE
CHM1_11165,663,579 - 65,665,098 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_001314   ⟸   NM_001323
- Peptide Label: precursor
- UniProtKB: Q15828 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSP00000311313   ⟸   ENST00000312134
Protein Domains
Cystatin

Promoters
RGD ID:7221113
Promoter ID:EPDNEW_H16302
Type:initiation region
Name:CST6_2
Description:cystatin E/M
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_H16303  
Experiment Methods:Single-end sequencing.; Paired-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh381166,011,491 - 66,011,551EPDNEW
RGD ID:7221115
Promoter ID:EPDNEW_H16303
Type:initiation region
Name:CST6_1
Description:cystatin E/M
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_H16302  
Experiment Methods:Single-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh381166,012,008 - 66,012,068EPDNEW

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 11q13.1-13.2(chr11:65741431-67705669)x1 copy number loss See cases [RCV000142881] Chr11:65741431..67705669 [GRCh38]
Chr11:65508902..67473140 [GRCh37]
Chr11:65265478..67229716 [NCBI36]
Chr11:11q13.1-13.2
pathogenic
GRCh37/hg19 11q13.1-13.2(chr11:64501919-67129258)x3 copy number gain See cases [RCV000511632] Chr11:64501919..67129258 [GRCh37]
Chr11:11q13.1-13.2
likely pathogenic
GRCh37/hg19 11p15.5-q25(chr11:230616-134938470) copy number gain See cases [RCV000511729] Chr11:230616..134938470 [GRCh37]
Chr11:11p15.5-q25
pathogenic
GRCh37/hg19 11p15.5-q25(chr11:230616-134938470)x3 copy number gain See cases [RCV000510881] Chr11:230616..134938470 [GRCh37]
Chr11:11p15.5-q25
pathogenic
GRCh37/hg19 11p15.5-q25(chr11:198510-134934063)x3 copy number gain not provided [RCV000737348] Chr11:198510..134934063 [GRCh37]
Chr11:11p15.5-q25
pathogenic
GRCh37/hg19 11p15.5-q25(chr11:70864-134938470)x3 copy number gain not provided [RCV000749874] Chr11:70864..134938470 [GRCh37]
Chr11:11p15.5-q25
pathogenic
GRCh37/hg19 11q13.1-13.2(chr11:65138976-67574402) copy number gain not provided [RCV000767601] Chr11:65138976..67574402 [GRCh37]
Chr11:11q13.1-13.2
pathogenic
NC_000011.9:g.(?_65633902)_(66115026_?)dup duplication Autosomal recessive cutis laxa type 1B [RCV000798155] Chr11:65866431..66347555 [GRCh38]
Chr11:65633902..66115026 [GRCh37]
Chr11:11q13.1-13.2
uncertain significance
NM_001323.4(CST6):c.361C>T (p.Gln121Ter) single nucleotide variant Ectodermal dysplasia 15, hypohidrotic/hair type [RCV000824677] Chr11:66012946 [GRCh38]
Chr11:65780417 [GRCh37]
Chr11:11q13.1
pathogenic
NM_001323.4(CST6):c.18C>T (p.Leu6=) single nucleotide variant not provided [RCV000888950] Chr11:66012062 [GRCh38]
Chr11:65779533 [GRCh37]
Chr11:11q13.1
likely benign

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:2478 AgrOrtholog
COSMIC CST6 COSMIC
Ensembl Genes ENSG00000175315 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSP00000311313 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENST00000312134 ENTREZGENE, UniProtKB/Swiss-Prot
GTEx ENSG00000175315 GTEx
HGNC ID HGNC:2478 ENTREZGENE
Human Proteome Map CST6 Human Proteome Map
InterPro Cystatin_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Prot_inh_cystat_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report hsa:1474 UniProtKB/Swiss-Prot
NCBI Gene 1474 ENTREZGENE
OMIM 601891 OMIM
  618535 OMIM
Pfam Cystatin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB PA26979 PharmGKB
PROSITE CYSTATIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART SM00043 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt CYTM_HUMAN UniProtKB/Swiss-Prot, ENTREZGENE
  Q6IBD2_HUMAN UniProtKB/TrEMBL
UniProt Secondary Q540N7 UniProtKB/Swiss-Prot